Comparing Partitions

How to cite this website



The framework of analysis used in this website was proposed in the following papers:

The combined use of Adjusted Rand and Wallace coefficients in microbial typing:

  • Carriço, J. A., C. Silva-Costa, J. Melo-Cristino, F. R. Pinto, H. de Lencastre, J. S. Almeida, and M. Ramirez. 2006. Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes. J. Clin. Microbiol. 44(7):2524-32. (link)

The proposal of Wallace's confidence intervals:

  • Pinto F.R., J. Melo-Cristino, and M. Ramirez. 2008. A Confidence Interval for the Wallace Coefficient of Concordance and Its Application to Microbial Typing Methods. PLoS ONE 3(11):e3696. doi:10.1371/journal.pone.0003696. (link)

The validation of jackknife for Confidence Intervals estimation:

  • Severiano A., J. Carriço, D. A. Robinson, M. Ramirez and F. R. Pinto. 2011. Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures. PLoS ONE.6(5):e19539. doi:10.1371/journal.pone.0019539 (link)

The proposal of an Adjusted Wallace:

  • Severiano A., F. R. Pinto, M. Ramirez and J. Carriço. 2011. Adjusted Wallace as a Measure of Congruence between Typing Methods. J. Clin. Microbiol. doi:10.1128/JCM.00624-11 (link)

The original references for the used coefficients are listed bellow.

References:


  1. Beisel, J.N., and J. C. Moreteau. 1997. A simple formula for caculating the lower limit of Shannon's diversity index. Ecol. Modell. 99:289-292.
  2. Carriço, J. A., C. Silva-Costa, J. Melo-Cristino, F. R. Pinto, H. de Lencastre, J. S. Almeida, and M. Ramirez. 2006. Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes. J. Clin. Microbiol. 44(7):2524-32. (link)
  3. Efron, B., and R.J. Tibshirani. 1993. An Introduction to the bootstrap. Monographs on Statistics and Applied Probability,Vol.57, Chapman & Hall/CRC.
  4. Fowlkes, E. B., and C. L. Mallows.1983. A method for comparing two hierarchical clusterings. J. Am. Stat. Assoc. 78:553-569.
  5. Grundmann, H., S. Hori, and G. Tanner. 2001. Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms. J. Clin. Microbiol. 39:4190-2. (link)
  6. Hill, M. 1973. Diversity and evenness: a unifying notation and its consequences. Ecology 54:427-432. (link)
  7. Hubert, L., and P. Arabie. 1985. Comparing partitions. J. Classif. 2:193-218. (link)
  8. Hunter, P. R., and M. A. Gaston. 1988. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26:2465-6. (link)
  9. Meila, M. 2005. Comparing clusterings - an axiomatic view. Proceedings of the Internation Machine learning Conference (ICML), ACM Pres, New York.
  10. Meila, M. 2007. Comparing clusterings - an information based distance. Journal of Multivariate Analysis. 98:873-895.
  11. Pinto, F. R., J. A. Carriço, M. Ramirez and J. S. Almeida. 2007. Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement. BMC Bioinf. 8:44. (link)
  12. Pinto, F.R., J. Melo-Cristino, M. Ramirez. 2008. A Confidence Interval for the Wallace Coefficient of Concordance and Its Application to Microbial Typing Methods. PLoS ONE 3(11):e3696. doi:10.1371/journal.pone.0003696. (link)
  13. Rand, W. M. 1971. Objective criteria for the evaluation of clustering methods. J. Am. Stat. Assoc. 66:846-850. (link)
  14. Severiano A., F. R. Pinto, M. Ramirez and J. Carriço. 2011. Adjusted Wallace as a Measure of Congruence between Typing Methods. J. Clin. Microbiol. doi:10.1128/JCM.00624-11 (link)
  15. Severiano A., J. Carriço, D. A. Robinson, M. Ramirez and F. R. Pinto. 2011. Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures. PLoS ONE.6(5):e19539. doi:10.1371/journal.pone.0019539 (link)
  16. Simpson, E. H. 1949. Measurement of species diversity. Nature. 163:688.
  17. Versalovic, J., V. Kapur, E. O. Mason, U. Shah, T. Koeuth, J. R. Lupski, and J. M. Musser. 1993. Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. J. Infect. Dis. 167:850-6.
  18. Wallace, D. L. 1983. A method for comparing two hierarchical clusterings: comment. J. Am. Stat. Assoc. 78:569-576. (link)


References that used the proposed framework/cited this website:


  1. Simões, A. S., L. Pereira, S. Nunes, A. Brito-Avô, H. de Lencastre, and R. Sá-Leão. 2011. Clonal evolution leading to maintenance of antibiotic resistance rates among colonizing pneumococci in the PCV7 era in Portugal. J. Clin. Microbiol. 49(8):2810-7.
  2. Martins, E. R., A. Andreu, et al. 2011. Group B streptococci causing neonatal infections in Barcelona are a stable clonal population: 18-year surveillance. J. Clin. Microbiol. 49(8):2911-8.
  3. Sá-Leão, R., F. R. Pinto, S. Aguiar, S. Nunes, J. A. Carriço, N. Frazão, N. Gonçalves-Sousa, J. Melo-Cristino, H. de Lencastre, and M. Ramirez. 2011. Analysis of invasiveness of pneumococcal serotypes and clones circulating in Portugal before widespread use of conjugate vaccines revealing heterogeneous behavior of clones expressing the same serotype. J. Clin. Microbiol. 49(4):1369-75.
  4. Tenover, F. C., T. Åkerlund, D. N. Gerding, R. V. Goering, T. Boström, A. Jonsson, E. Wong, A. T. Wortman, and D. H. Persing. 2011. Comparison of Strain Typing Results for Clostridium difficile Isolates from North America. J. Clin. Microbiol. 49(5):1831-7.
  5. Elberse, K. E. M., S. Nunes, R. Sá-Leão, H. G. J. van der Heide, L. M. Schouls. 2011. Multiple-Locus Variable Number Tandem Repeat Analysis for Streptococcus pneumoniae: Comparison with PFGE and MLST. Plos ONE. 6(5):e19668.
  6. Al Nakiba, M., M. Longob, A. Tazia, A. Billoeta, J. Raymonda, P. Trieu-Cuote, and C. Poyart. 2011. Comparison of the Diversilab® system with multi-locus sequence typing and pulsed-field gel electrophoresis for the characterization of Streptococcus agalactiae invasive strains. J. Microbiol. Methods 85(2):137-42.
  7. Milheiriço, C., A. Portelinha, L. Krippah, H. de Lencastre, and D. C. Oliveira. 2011. Evidence for a purifying selection acting on the β-lactamase locus in epidemic clones of methicillin-resistant Staphylococcus aureus. BMC Microbiol. 11:76.
  8. Muñoz-Almagroa, C., P. Ciruela, et al. 2011. Serotypes and clones causing invasive pneumococcal disease before the use of new conjugate vaccines in Catalonia, Spain. J. Infect. 63(2):151-62.
  9. Behringer, M., W. G. Miller and O. A. Oyarzaba. 2011. Typing of Campylobacter jejuni and Campylobacter coli isolated from live broilers and retail broiler meat by flaA-RFLP, MLST, PFGE and REP-PCR. J. Microbiol. Methods 84:194-201.
  10. Babouee B., R. Frei, E. Schultheiss, A. F. Widmer and D. Goldenberger. 2011. Comparison of the rep-PCR system DiversiLab with spa typing and pulsed-field gel electrophoresis for the clonal characterization of methicillin-resistant Staphylococcus aureus.J. Clin. Microbiol. 49(4):1549-55.
  11. Vainio, A., S. Koskela, A. virolainen, J. Vuopio and S. Salmenlinna. 2011. Adapting spa typing for functional laboratory-based surveillance of methicillin-resistant Staphylococcus aureus. Eur. J. Clin. Microbiol. Infect. Dis. 30(6):789-97.
  12. Sadowy, E., A. Kuch, M. Gniadkowski et al. 2010. Expansion and evolution of the Streptococcus pneumoniae Spain9V-ST156 clonal complex in Poland. Antimicrob. Agents Chemother. 54(5):1720-1727.
  13. van Mansfeld R., I. Jongerden, M. Bootsma, A. Buiting, M. Bonten and R. Willems. 2010. The population genetics of Pseudomonas aeruginosa isolates from different patient populations exhibits high-level host specificity. PLoS ONE 5(10):e13482.
  14. Hauser E, E. Tietze, R. Helmuth, E. Junker, K. Blank, R. Prager, W. Rabsch, B. Appel, A. Fruth, B. Malorny. 2010. Pork contaminated with Salmonella enterica serovar 4,[5],12:i:-, an emerging health risk for humans. Appl. Environ. Microbiol. 76(14):4601-10.
  15. McLernon, J., E. Costello, O. Flynn et al.2010. Evaluation of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat analysis and spoligotyping for genotyping of Mycobacterium bovis isolates and a comparison with restriction fragment length polymorphism typing. J. Clin. Microbiol. 48(12):4541-4545
  16. Marsh, W. M., M. M. O'Leary, K. A. Shutt et al. 2010. Multilocus Variable-Number Tandem-Repeat analysis and Multilocus Sequence typing Reveal Genetic Relashionships among clostridium difficile Isolates Genotyped by Restriction Endonuclease Analysis. J. Clin. Microbiol. 48(2):412-418
  17. Aguiar, S. I., F. R. Pinto, S. Nunes, I. Serrano, J. Melo-Cristino, R. Sa-Leao, M. Ramirez, and H. de Lencastre. 2010. Denmark14-230 Clone as an Increasing Cause of Pneumococcal Infection in Portugal within a Background of Diverse Serotype 19A Lineages. J. Clin. Microbiol. 48:101-108.
  18. Costa, J. M., D. Garcia-Hermoso, M. Olivi, O. Cabaret, C. Farrugia, G. Lecellier, F. Dromer, and S. Bretagne. 2010. Genotyping of Candida albicans using length fragment and high-resolution melting analyses together with minisequencing of a polymorphic microsatellite locus. J. Microbiol. Methods 80:306-309.
  19. Diancourt, L., V. Passet, A. Nemec, L. Dijkshoorn and S. Brisse. 2010. The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool. PLoS ONE 5(4):e10034. doi:10.1371/journal.pone.0010034
  20. Martins, E. R., J. Melo-Cristino, and M. Ramirez. 2010. Evidence for Rare Capsular Switching in Streptococcus agalactiae. J. Bacteriol. 192:1361-1369.
  21. Shore, A. C., A. S. Rossney, P. M. Kinnevey, O. M. Brennan, E. Creamer, O. Sherlock, A. Dolan, R. Cunney, D. J. Sullivan, R. V. Goering, H. Humphreys, and D. C. Coleman. 2010. Enhanced Discrimination of Highly Clonal ST22-Methicillin-Resistant Staphylococcus aureus IV Isolates Achieved by Combining spa, dru, and Pulsed-Field Gel Electrophoresis Typing Data. J. Clin. Microbiol. 48:1839-1852.
  22. Pinho, M. D., J. Melo-Cristino, M. Ramirez, and S. Portuguese Grp Study. 2010. Fluoroquinolone Resistance in Streptococcus dysgalactiae subsp equisimilis and Evidence for a Shared Global Gene Pool with Streptococcus pyogenes. Antimicrob. Agents Chemother. 54:1769-1777.
  23. Carrolo, M., F. R. Pinto, J. Melo-Cristino, and M. Ramirez. 2009. Pherotypes are driving genetic differentiation within Streptococcus pneumoniae. BMC Microbiol. 9.
  24. Rasschaert, G., W. Vanderhaeghen, I. Dewaele, N. Janez, X. Huijsdens, P. Butaye, and M. Heyndrickx. 2009. Comparison of Fingerprinting Methods for Typing Methicillin-Resistant Staphylococcus aureus Sequence Type 398. J. Clin. Microbiol. 47:3313-3322.
  25. Chowdhury, S. A., C. A. Arias, S. R. Nallapareddy, J. Reyes, R. J. L. Willems, and B. E. Murray. 2009. A Trilocus Sequence Typing Scheme for Hospital Epidemiology and Subspecies Differentiation of an Important Nosocomial Pathogen, Enterococcus faecalis. J. Clin. Microbiol. 47:2713-2719.
  26. Conceicao, T., M. A. de Sousa, and H. de Lencastre. 2009. Staphylococcal Interspersed Repeat Unit Typing of Staphylococcus aureus: Evaluation of a New Multilocus Variable-Number Tandem-Repeat Analysis Typing Method. J. Clin. Microbiol. 47:1300-1308.
  27. McTavish, S. M., C. E. Pope, C. Nicol, D. Campbell, N. French, and P. E. Carter. 2009. Multilocus sequence typing of Campylobacter jejuni, and the correlation between clonal complex and pulsed-field gel electrophoresis macrorestriction profile. FEMS Microbiol. Lett. 298:149-156.
  28. Zaiss, N. H., M. Rupnik, E. J. Kuijper, C. Harmanus, D. Michielsen, K. Janssens, and U. Nubel. 2009. Typing Clostridium difficile strains based on tandem repeat sequences. BMC Microbiol. 9.
  29. Rodrigues, F., S. Nunes, R. Sa-Leao, G. Goncalves, L. Lemos, and H. de Lencastre. 2009. Streptococcus pneumoniae Nasopharyngeal Carriage in Children Attending Day-Care Centers in the Central Region of Portugal, In the Era of 7-Valent Pneumococcal Conjugate Vaccine. Microb. Drug Resist. 15:269-277.
  30. Silva, E., S. Leitao, T. Tenreiro, C. Pomba, T. Nunes, L. L. da Costa, and L. Mateus. 2009. Genomic and phenotypic characterization of Escherichia coli isolates recovered from the uterus of puerperal dairy cows. J. Dairy Sci. 92:6000-6010.
  31. Faria, N. A., J. A. Carrico, D. C. Oliveira, M. Ramirez, and H. de Lencastre. 2008. Analysis of typing methods for epidemiological surveillance of both methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains. J. Clin. Microbiol. 46:136-144.
  32. Miragaia, M., J. A. Carrico, J. C. Thomas, I. Couto, M. C. Enright, and H. de Lencastre. 2008. Comparison of molecular typing methods for characterization of Staphylococcus epidermidis: Proposal for clone definition. J. Clin. Microbiol. 46:118-129.
  33. Erlandsson, M., H. Gill, D. Nordlinder, C. G. Giske, D. Jonas, L. E. Nilsson, S. Walther, and H. Hanberger. 2008. Antibiotic susceptibility patterns and clones of Pseudomonas aeruginosa in Swedish ICUs. Scand. J. Infect. Dis. 40:487-494.
  34. Silva-Costa, C., F. R. Pinto, M. Ramirez, J. Melo-Cristino, and S. Portuguese Surveillance Grp. 2008. Decrease in macrolide resistance and clonal instability among Streptococcus pyogenes in Portugal. Clin. Microbiol. Infect. 14:1152-1159.
  35. Aguiar, S. I., I. Serrano, F. R. Pinto, J. Melo-Cristino, and M. Ramirez. 2008. The presence of the pilus locus is a clonal property among pneumococcal invasive isolates. BMC Microbiol. 8.
  36. Vimont, S., B. Mnif, C. Fevre and S. Brisse. 2008. Comparison of PFGE and multilocus sequence typing for analysis of Klebsiella pneumoniae isolates. J. Med. Microbiol. 57(10):1308-10.
  37. Vainio, A., M. Karden-Lilja, S. Ibrahem, A. M. Kerttula, S. Salmenlinna, A. Virolainen, and J. Vuopio-Varkila. 2008. Clonality of epidemic methicillin-resistant Staphylococcus aureus strains in Finland as defined by several molecular methods. Eur. J. Clin. Microbiol. Infect. Dis. 27:545-555.
  38. Martins, E. R., M. A. Pessanha, M. Ramirez, J. Melo-Cristino, and S. Portuguese Grp Study. 2007. Analysis of group B streptococcal isolates from infants and pregnant women in Portugal revealing two lineages with enhanced invasiveness. J. Clin. Microbiol. 45:3224-3229.
  39. Friaes, A., M. Ramirez, J. Melo-Cristino, and S. Portuguese Grp Study. 2007. Nonoutbreak surveillance of group A streptococci causing invasive disease in Portugal identified internationally disseminated clones among members of a genetically heterogeneous population. J. Clin. Microbiol. 45:2044-2047.
  40. van Belkum, A., P. T. Tassios, L. Dijkshoorn, S. Haeggman, B. Cookson, et al. 2007. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin. Microbiol. Infect. 13:1-46.




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